R help - Mar 2011 - read.table() with "\t" as seperator, all other programs report equal fields each row, read.table() returns unequal row length error

hi, list

R is undoudtedly my favorite statistic tool, however, the data
inputnpart has long been a pain. most data I have to deal with are
irregular and contains special character.

Recently I get a tab delimited data, read.table(filename,sep="\t")
constantly return erors for certain rows does not has xyz elements
while all other programs such as perl,python, awk all report equal row
length if use "\t" as seperator.

I scout through the problematic row, sometimes it is because a row
contains a "#", so I go back to specify comment.char=""
next it will be some other problems, for some rows I simply can't
figure out what the problem is.

can I have any guru suggestion to save this pain now and in the
future, is CSV a safer format? or can anyone let me know what are the
fundamental principles I must bear in mind when do preliminary data
processing using other programs such as perl to ensure the output can
be readily feed into R.

best

yong

On Mar 16, 2011, at 17:37 , Yong Wang wrote:
> hi, list
> 
> R is undoudtedly my favorite statistic tool, however, the data
> inputnpart has long been a pain. most data I have to deal with are
> irregular and contains special character.
> 
> Recently I get a tab delimited data,
read.table(filename,sep="\t")
> constantly return erors for certain rows does not has xyz elements
> while all other programs such as perl,python, awk all report equal row
> length if use "\t" as seperator.
> 
> I scout through the problematic row, sometimes it is because a row
> contains a "#", so I go back to specify comment.char=""
> next it will be some other problems, for some rows I simply can't
> figure out what the problem is.
> 
> can I have any guru suggestion to save this pain now and in the
> future, is CSV a safer format? or can anyone let me know what are the
> fundamental principles I must bear in mind when do preliminary data
> processing using other programs such as perl to ensure the output can
> be readily feed into R.
A couple of other things can get messed up, e.g. quote symbols. Does
read.delim()/read.delim2() perhaps work better?

With CSV, you generally get the same sort of issues, just with ","
instead of "\t".

> 
> best
> 
> yong
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
-- 
Peter Dalgaard
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com